Mercurial > repos > iuc > trinity_align_and_estimate_abundance
comparison align_and_estimate_abundance.xml @ 0:a21e229da9a1 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
author | iuc |
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date | Mon, 01 Aug 2016 14:43:15 -0400 |
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children | a966877db15b |
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1 <tool id="trinity_align_and_estimate_abundance" name="Align reads and estimate abundance" version="@WRAPPER_VERSION@.0"> | |
2 <description>on a de novo assembly of RNA-Seq data</description> | |
3 <macros> | |
4 <import>macros.xml</import> | |
5 </macros> | |
6 <expand macro="requirements"> | |
7 <requirement type="package" version="1.1.2">bowtie</requirement> | |
8 <requirement type="package" version="2.2.6">bowtie2</requirement> | |
9 <requirement type="package" version="1.2">samtools</requirement> | |
10 <requirement type="package" version="1.2.28">rsem</requirement> | |
11 <requirement type="package" version="1.5.1">eXpress</requirement> | |
12 <requirement type="package" version="0.6.0">salmon</requirement> | |
13 </expand> | |
14 <expand macro="stdio"/> | |
15 <command><![CDATA[ | |
16 ln -s '$transcripts' input.fa && | |
17 | |
18 #if $inputs.paired_or_single == "paired": | |
19 #if $inputs.left_input.is_of_type('fasta'): | |
20 ln -s '$inputs.left_input' paired_left.fa && | |
21 ln -s '$inputs.right_input' paired_right.fa | |
22 #else: | |
23 ln -s '$inputs.left_input' paired_left.fq && | |
24 ln -s '$inputs.right_input' paired_right.fq | |
25 #end if | |
26 #else: | |
27 #if $inputs.left_input.is_of_type('fasta'): | |
28 ln -s '$inputs.input' single.fa | |
29 #else: | |
30 ln -s '$inputs.input' single.fq | |
31 #end if | |
32 #end if | |
33 | |
34 && | |
35 | |
36 align_and_estimate_abundance.pl | |
37 | |
38 --transcripts input.fa | |
39 | |
40 --est_method $method.est_method | |
41 #if $method.est_method == "RSEM" or $method.est_method == "eXpress": | |
42 --aln_method $method.aln_method | |
43 #else if $method.est_method == "salmon": | |
44 --salmon_idx_type $method.salmon_idx_type | |
45 #end if | |
46 | |
47 #if $inputs.paired_or_single == "paired": | |
48 | |
49 #if $inputs.left_input.is_of_type('fasta'): | |
50 --left paired_left.fa --right paired_right.fa --seqType fa | |
51 #else: | |
52 --left paired_left.fq --right paired_right.fq --seqType fq | |
53 #end if | |
54 | |
55 #if $inputs.strand.is_strand_specific: | |
56 --SS_lib_type $inputs.strand.library_type | |
57 #end if | |
58 | |
59 --max_ins_size $inputs.paired_fragment_length | |
60 | |
61 #else: | |
62 #if $inputs.input.is_of_type('fasta'): | |
63 --single single.fa --seqType fa | |
64 #else: | |
65 --single single.fq --seqType fq | |
66 #end if | |
67 | |
68 #if $inputs.strand.is_strand_specific: | |
69 --SS_lib_type $inputs.strand.library_type | |
70 #end if | |
71 #end if | |
72 | |
73 ## Additional parameters. | |
74 #if $additional_params.gene_map.has_gene_map == "no": | |
75 --gene_trans_map $additional_params.gene_map.gene_trans_map | |
76 #else | |
77 --trinity_mode | |
78 #end if | |
79 | |
80 --prep_reference | |
81 | |
82 --output_dir output | |
83 | |
84 ## CPU | |
85 --thread_count \${GALAXY_SLOTS:-4} | |
86 ]]></command> | |
87 <inputs> | |
88 <param format="fasta" name="transcripts" argument="--transcripts" type="data" label="Transcripts" help="de novo assembly of RNA-Seq data"/> | |
89 <conditional name="inputs"> | |
90 <param name="paired_or_single" type="select" label="Paired or Single-end data?"> | |
91 <option value="paired">Paired</option> | |
92 <option value="single">Single</option> | |
93 </param> | |
94 <when value="paired"> | |
95 <param format="fasta,fastqsanger" name="left_input" argument="--left" type="data" label="Left/Forward strand reads" help=""/> | |
96 <param format="fasta,fastqsanger" name="right_input" argument="--right" type="data" label="Right/Reverse strand reads" help=""/> | |
97 <conditional name="strand"> | |
98 <param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/> | |
99 <when value="false"> | |
100 </when> | |
101 <when value="true"> | |
102 <param name="library_type" argument="--SS_lib_type" type="select" label="Strand-specific Library Type"> | |
103 <option value="FR">Forward-Reverse</option> | |
104 <option value="RF">Reverse-Forward</option> | |
105 </param> | |
106 </when> | |
107 </conditional> | |
108 <param name="paired_fragment_length" argument="--max_ins_size" type="integer" value="800" min="1" label="Maximum insert size" help="bowtie -X parameter"/> | |
109 </when> | |
110 <when value="single"> | |
111 <param format="fasta,fastqsanger" argument="--single" name="input" type="data" label="Single-end reads" help=""/> | |
112 <conditional name="strand"> | |
113 <param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/> | |
114 <when value="false"> | |
115 </when> | |
116 <when value="true"> | |
117 <param name="library_type" argument="--SS_lib_type" type="select" label="Strand-specific Library Type"> | |
118 <option value="F">F</option> | |
119 <option value="R">R</option> | |
120 </param> | |
121 </when> | |
122 </conditional> | |
123 </when> | |
124 </conditional> | |
125 | |
126 <conditional name="method"> | |
127 <param type="select" name="est_method" argument="--est_method" label="Abundance estimation method"> | |
128 <option value="RSEM">RSEM</option> | |
129 <option value="eXpress">eXpress</option> | |
130 <option value="salmon">Salmon</option> | |
131 </param> | |
132 <when value="RSEM"> | |
133 <param type="select" name="aln_method" argument="--aln_method" label="Alignment method"> | |
134 <option value="bowtie">Bowtie</option> | |
135 <option value="bowtie2">Bowtie2</option> | |
136 </param> | |
137 </when> | |
138 <when value="eXpress"> | |
139 <param type="select" name="aln_method" argument="--aln_method" label="Alignment method"> | |
140 <option value="bowtie">Bowtie</option> | |
141 <option value="bowtie2">Bowtie2</option> | |
142 </param> | |
143 </when> | |
144 <when value="salmon"> | |
145 <param type="select" name="salmon_idx_type" argument="--salmon_idx_type" label="Index type"> | |
146 <option value="quasi">Quasi</option> | |
147 <option value="fmd">FMD</option> | |
148 </param> | |
149 </when> | |
150 </conditional> | |
151 | |
152 <section name="additional_params" title="Additional Options" expanded="False"> | |
153 <conditional name="gene_map"> | |
154 <param name="has_gene_map" type="select" label="Trinity assembly?" help="If the transcripts were not assembled by trinity, additional information is needed"> | |
155 <option value="yes">Yes</option> | |
156 <option value="no">No</option> | |
157 </param> | |
158 <when value="yes"> | |
159 </when> | |
160 <when value="no"> | |
161 <param format="tabular" name="gene_trans_map" argument="--gene_trans_map" type="data" label="Gene to transcript correspondence ('gene(tab)transcript' lines)" /> | |
162 </when> | |
163 </conditional> | |
164 | |
165 </section> | |
166 </inputs> | |
167 <outputs> | |
168 <data format="tabular" name="isoforms_counts_rsem" label="${tool.name} on ${on_string}: isoforms counts" from_work_dir="output/RSEM.isoforms.results"> | |
169 <filter>method['est_method'] == "RSEM"</filter> | |
170 </data> | |
171 <data format="tabular" name="genes_counts_rsem" label="${tool.name} on ${on_string}: genes counts" from_work_dir="output/RSEM.genes.results"> | |
172 <filter>method['est_method'] == "RSEM"</filter> | |
173 </data> | |
174 | |
175 <data format="tabular" name="isoforms_counts_express" label="${tool.name} on ${on_string}: isoforms counts" from_work_dir="output/results.xprs"> | |
176 <filter>method['est_method'] == "eXpress"</filter> | |
177 </data> | |
178 <data format="tabular" name="genes_counts_express" label="${tool.name} on ${on_string}: genes counts" from_work_dir="output/results.xprs.genes"> | |
179 <filter>method['est_method'] == "eXpress"</filter> | |
180 </data> | |
181 | |
182 <data format="tabular" name="isoforms_counts_salmon" label="${tool.name} on ${on_string}: isoforms counts" from_work_dir="output/quant.sf"> | |
183 <filter>method['est_method'] == "salmon"</filter> | |
184 </data> | |
185 <data format="tabular" name="genes_counts_salmon" label="${tool.name} on ${on_string}: genes counts" from_work_dir="output/quant.sf.genes"> | |
186 <filter>method['est_method'] == "salmon"</filter> | |
187 </data> | |
188 </outputs> | |
189 <tests> | |
190 <test> | |
191 <param name="paired_or_single" value="paired"/> | |
192 <param name="left_input" value="reads.left.fq"/> | |
193 <param name="right_input" value="reads.right.fq"/> | |
194 <param name="transcripts" value="raw/Trinity.fasta"/> | |
195 <param name="library_type" value="RF"/> | |
196 <param name="est_method" value="RSEM"/> | |
197 <param name="aln_method" value="bowtie"/> | |
198 <param name="has_gene_map" value="yes"/> | |
199 <output name="isoforms_counts_rsem"> | |
200 <assert_contents> | |
201 <has_line_matching expression="TRINITY_DN0_c0_g1_i1	.*" /> | |
202 <has_n_columns n="8" /> | |
203 </assert_contents> | |
204 </output> | |
205 <output name="genes_counts_rsem"> | |
206 <assert_contents> | |
207 <has_line_matching expression="TRINITY_DN0_c0_g1	.*" /> | |
208 <has_n_columns n="7" /> | |
209 </assert_contents> | |
210 </output> | |
211 </test> | |
212 <test> | |
213 <param name="paired_or_single" value="paired"/> | |
214 <param name="left_input" value="reads.left.fq"/> | |
215 <param name="right_input" value="reads.right.fq"/> | |
216 <param name="transcripts" value="raw/Trinity.fasta"/> | |
217 <param name="library_type" value="RF"/> | |
218 <param name="est_method" value="RSEM"/> | |
219 <param name="aln_method" value="bowtie2"/> | |
220 <param name="has_gene_map" value="yes"/> | |
221 <output name="isoforms_counts_rsem"> | |
222 <assert_contents> | |
223 <has_line_matching expression="TRINITY_DN0_c0_g1_i1	.*" /> | |
224 <has_n_columns n="8" /> | |
225 </assert_contents> | |
226 </output> | |
227 <output name="genes_counts_rsem"> | |
228 <assert_contents> | |
229 <has_line_matching expression="TRINITY_DN0_c0_g1	.*" /> | |
230 <has_n_columns n="7" /> | |
231 </assert_contents> | |
232 </output> | |
233 </test> | |
234 <test> | |
235 <param name="paired_or_single" value="paired"/> | |
236 <param name="left_input" value="reads.left.fq"/> | |
237 <param name="right_input" value="reads.right.fq"/> | |
238 <param name="transcripts" value="raw/Trinity.fasta"/> | |
239 <param name="library_type" value="RF"/> | |
240 <param name="est_method" value="eXpress"/> | |
241 <param name="aln_method" value="bowtie"/> | |
242 <param name="has_gene_map" value="yes"/> | |
243 <output name="isoforms_counts_express"> | |
244 <assert_contents> | |
245 <has_line_matching expression=".*	TRINITY_DN2_c3_g1_i1	.*" /> | |
246 <has_n_columns n="15" /> | |
247 </assert_contents> | |
248 </output> | |
249 <output name="genes_counts_express"> | |
250 <assert_contents> | |
251 <has_line_matching expression="NA	TRINITY_DN3_c0_g1.*" /> | |
252 <has_n_columns n="15" /> | |
253 </assert_contents> | |
254 </output> | |
255 </test> | |
256 <test> | |
257 <param name="paired_or_single" value="paired"/> | |
258 <param name="left_input" value="reads.left.fq"/> | |
259 <param name="right_input" value="reads.right.fq"/> | |
260 <param name="transcripts" value="raw/Trinity.fasta"/> | |
261 <param name="library_type" value="RF"/> | |
262 <param name="est_method" value="salmon"/> | |
263 <param name="aln_method" value="bowtie"/> | |
264 <param name="has_gene_map" value="yes"/> | |
265 <output name="isoforms_counts_salmon"> | |
266 <assert_contents> | |
267 <has_line_matching expression="TRINITY_DN2_c3_g1_i1	.*" /> | |
268 <has_n_columns n="5" /> | |
269 </assert_contents> | |
270 </output> | |
271 <output name="genes_counts_salmon"> | |
272 <assert_contents> | |
273 <has_line_matching expression="TRINITY_DN3_c0_g1.*" /> | |
274 <has_n_columns n="5" /> | |
275 </assert_contents> | |
276 </output> | |
277 </test> | |
278 </tests> | |
279 <help> | |
280 <![CDATA[ | |
281 Trinity_ assembles transcript sequences from Illumina RNA-Seq data. | |
282 This tool estimates the abundance of isoforms and genes of a transcriptome assembled with Trinity, using FastQ of a specific sample. | |
283 | |
284 **Inputs** | |
285 | |
286 It takes as input a transcriptome assembled with Trinity and the reads from a RNASeq sample. | |
287 You have to choose between several counting methods. | |
288 | |
289 If you dont align on a Trinity assembly, you need to provide a file of the following (tabular) format to map gene ids to transcript ids: | |
290 | |
291 =========== ================ | |
292 gene1 transcript1 | |
293 ----------- ---------------- | |
294 gene2 transcript2 | |
295 =========== ================ | |
296 | |
297 **Output** | |
298 | |
299 This tool will produce 2 tabular files, with counts for isoforms and genes respectively. More details on this page: | |
300 | |
301 .. _Trinity manual: https://github.com/trinityrnaseq/trinityrnaseq/wiki/Trinity-Transcript-Quantification | |
302 | |
303 | |
304 .. _Trinity: http://trinityrnaseq.github.io | |
305 ]]> | |
306 </help> | |
307 | |
308 <expand macro="citation" /> | |
309 </tool> |